Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals

Mellor, Kate C., Blackwell, Grace A., Cawthraw, Shaun A., Mensah, Nana E., Reid, Stuart W. J., Thomson, Nicholas R., Petrovska, Liljana and Mather, Alison E. (2022) Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals. Microbial Genomics, 8 (8). ISSN 2057-5858

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Abstract

Plasmids are mobile elements that can carry genes encoding traits of clinical concern, including antimicrobial resistance (AMR) and virulence. Population-level studies of Enterobacterales, including Escherichia coli, Shigella and Klebsiella, indicate that plasmids are important drivers of lineage expansions and dissemination of AMR genes. Salmonella Typhimurium is the second most common cause of salmonellosis in humans and livestock in the UK and Europe. The long-term dynamics of plasmids between S. Typhimurium were investigated using isolates collected through national surveillance of animals in England and Wales over a 25-year period. The population structure of S. Typhimurium and its virulence plasmid (where present) were inferred through phylogenetic analyses using whole-genome sequence data for 496 isolates. Antimicrobial resistance genes and plasmid markers were detected in silico. Phenotypic plasmid characterization, using the Kado and Liu method, was used to confirm the number and size of plasmids. The differences in AMR and plasmids between clades were striking, with livestock clades more likely to carry one or more AMR plasmid and be multi-drug-resistant compared to clades associated with wildlife and companion animals. Multiple small non-AMR plasmids were distributed across clades. However, all hybrid AMR-virulence plasmids and most AMR plasmids were highly clade-associated and persisted over decades, with minimal evidence of horizontal transfer between clades. This contrasts with the role of plasmids in the short-term dissemination of AMR between diverse strains in other Enterobacterales in high-antimicrobial-use settings, with implications for predicting plasmid dissemination amongst S. Typhimurium.

Item Type: Article
Additional Information: Funding information: K.C.M. was supported by a Bloomsbury PhD. scholarship, Royal Veterinary College and London School of Hygiene and Tropical Medicine. A.E.M. is a Food Standards Agency Fellow and is supported by a Biotechnology and Biological Sciences Research Council Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain). Data collection at the Animal and Plant Health Agency and whole-genome sequencing were funded by DEFRA project RDOZO347. This research was funded in whole, or in part, by the Wellcome Trust (grant number 206 194).
Uncontrolled Keywords: antimicrobial resistance,plasmids,salmonella typhimurium,surveillance,epidemiology,microbiology,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/2700/2713
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Depositing User: LivePure Connector
Date Deposited: 04 Nov 2022 16:30
Last Modified: 04 Nov 2022 16:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/89626
DOI: 10.1099/mgen.0.000826

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